Multiple sequence alignment - TraesCS4D01G229400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G229400 chr4D 100.000 7772 0 0 1 7772 389232081 389224310 0.000000e+00 14353.0
1 TraesCS4D01G229400 chr4D 82.210 371 46 13 1 365 362071202 362070846 1.270000e-77 302.0
2 TraesCS4D01G229400 chr4D 94.444 54 2 1 3147 3200 40845340 40845288 1.800000e-11 82.4
3 TraesCS4D01G229400 chr4A 94.867 4909 137 25 2929 7772 70811798 70806940 0.000000e+00 7563.0
4 TraesCS4D01G229400 chr4A 94.764 2292 63 11 637 2877 70814084 70811799 0.000000e+00 3515.0
5 TraesCS4D01G229400 chr4A 86.405 662 49 21 2 653 70824724 70824094 0.000000e+00 686.0
6 TraesCS4D01G229400 chr4B 94.767 4644 132 42 3192 7772 479155283 479150688 0.000000e+00 7127.0
7 TraesCS4D01G229400 chr4B 93.583 1418 50 6 1524 2900 479157008 479155591 0.000000e+00 2076.0
8 TraesCS4D01G229400 chr4B 92.894 1154 52 13 309 1437 479158683 479157535 0.000000e+00 1650.0
9 TraesCS4D01G229400 chr4B 94.981 259 11 1 2900 3156 479155541 479155283 9.390000e-109 405.0
10 TraesCS4D01G229400 chr4B 82.133 375 47 13 1 367 416449172 416449534 3.520000e-78 303.0
11 TraesCS4D01G229400 chr4B 87.059 85 6 5 2850 2931 71592018 71591936 2.990000e-14 91.6
12 TraesCS4D01G229400 chr7A 84.309 376 34 17 1 365 340853663 340853302 2.080000e-90 344.0
13 TraesCS4D01G229400 chr7B 83.820 377 42 9 2 366 408819673 408820042 2.690000e-89 340.0
14 TraesCS4D01G229400 chr7B 82.181 376 48 13 1 367 52497776 52497411 9.800000e-79 305.0
15 TraesCS4D01G229400 chr7B 96.875 32 1 0 3174 3205 667483089 667483120 4.000000e-03 54.7
16 TraesCS4D01G229400 chr6B 83.602 372 46 10 2 366 477782584 477782221 1.250000e-87 335.0
17 TraesCS4D01G229400 chr6B 82.493 377 40 14 1 365 195199686 195200048 2.720000e-79 307.0
18 TraesCS4D01G229400 chr6B 82.633 357 39 15 14 366 445467967 445467630 2.120000e-75 294.0
19 TraesCS4D01G229400 chr6B 89.157 83 5 4 2866 2946 542928641 542928721 4.960000e-17 100.0
20 TraesCS4D01G229400 chr6B 96.970 33 0 1 3147 3179 151608229 151608260 4.000000e-03 54.7
21 TraesCS4D01G229400 chr6B 100.000 29 0 0 3147 3175 437482936 437482964 4.000000e-03 54.7
22 TraesCS4D01G229400 chr5D 83.598 378 41 12 2 366 305434641 305435010 1.250000e-87 335.0
23 TraesCS4D01G229400 chr5B 83.696 368 43 12 8 367 447317204 447316846 1.620000e-86 331.0
24 TraesCS4D01G229400 chr1D 83.155 374 44 9 2 363 184826557 184826923 2.700000e-84 324.0
25 TraesCS4D01G229400 chr5A 91.781 73 4 2 2874 2946 66844407 66844337 4.960000e-17 100.0
26 TraesCS4D01G229400 chr5A 94.444 36 0 2 3147 3182 651563575 651563542 4.000000e-03 54.7
27 TraesCS4D01G229400 chr3A 93.750 64 3 1 2882 2944 71515918 71515855 2.310000e-15 95.3
28 TraesCS4D01G229400 chr2D 94.737 57 2 1 3147 3202 87242227 87242171 3.860000e-13 87.9
29 TraesCS4D01G229400 chr2D 86.885 61 3 4 2875 2933 441531489 441531546 6.510000e-06 63.9
30 TraesCS4D01G229400 chr3D 92.727 55 2 2 2886 2939 62783321 62783268 2.330000e-10 78.7
31 TraesCS4D01G229400 chr7D 90.000 60 3 3 2872 2931 412016522 412016466 3.010000e-09 75.0
32 TraesCS4D01G229400 chr7D 90.741 54 2 1 3147 3200 592075611 592075561 1.400000e-07 69.4
33 TraesCS4D01G229400 chr7D 85.246 61 6 3 2871 2931 412016462 412016519 8.420000e-05 60.2
34 TraesCS4D01G229400 chr6A 88.000 50 4 2 2853 2900 507116545 507116496 3.030000e-04 58.4
35 TraesCS4D01G229400 chr2B 100.000 29 0 0 3147 3175 413450528 413450556 4.000000e-03 54.7
36 TraesCS4D01G229400 chr2B 96.875 32 0 1 3147 3178 68226842 68226812 1.400000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G229400 chr4D 389224310 389232081 7771 True 14353.0 14353 100.00000 1 7772 1 chr4D.!!$R3 7771
1 TraesCS4D01G229400 chr4A 70806940 70814084 7144 True 5539.0 7563 94.81550 637 7772 2 chr4A.!!$R2 7135
2 TraesCS4D01G229400 chr4A 70824094 70824724 630 True 686.0 686 86.40500 2 653 1 chr4A.!!$R1 651
3 TraesCS4D01G229400 chr4B 479150688 479158683 7995 True 2814.5 7127 94.05625 309 7772 4 chr4B.!!$R2 7463


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
470 475 0.318699 CTTCCAGCGACGTCTCACAA 60.319 55.000 14.70 0.00 0.00 3.33 F
1482 1513 0.322008 CCCAGTCAGAAGCCTGGTTC 60.322 60.000 5.09 0.91 45.61 3.62 F
1487 1518 1.531578 GTCAGAAGCCTGGTTCGTTTC 59.468 52.381 3.66 0.00 40.76 2.78 F
2118 2589 1.912043 CAGGGAGGGAGAATCACAAGT 59.088 52.381 0.00 0.00 45.06 3.16 F
3284 3849 1.562942 TCTCTTCCTCCTGCATTGCAT 59.437 47.619 12.53 0.00 38.13 3.96 F
3834 4400 1.407575 GGTAGCAAAGGAGCCTCTTCC 60.408 57.143 0.00 0.00 37.52 3.46 F
4276 4842 3.019564 GCTAGCTTCATCACCCAACAAT 58.980 45.455 7.70 0.00 0.00 2.71 F
5801 6374 0.179037 GCAGCCAGCTCATACATCCA 60.179 55.000 0.00 0.00 41.15 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2633 0.042131 TGTAAGGAGGGGACATCGGT 59.958 55.000 0.00 0.00 0.00 4.69 R
3178 3743 2.065799 ACTCCCTCTGTCCCAAAATGT 58.934 47.619 0.00 0.00 0.00 2.71 R
3179 3744 2.887151 ACTCCCTCTGTCCCAAAATG 57.113 50.000 0.00 0.00 0.00 2.32 R
3813 4379 1.279271 GAAGAGGCTCCTTTGCTACCA 59.721 52.381 11.71 0.00 0.00 3.25 R
5003 5574 0.399454 AGACATCAGCCACTGCAACT 59.601 50.000 0.00 0.00 41.13 3.16 R
5460 6032 5.478332 CAGGAATAAGGACCTCAAAAGCTTT 59.522 40.000 5.69 5.69 33.91 3.51 R
6259 6832 2.217429 TTCGGGCTGCAAAAAGAAAC 57.783 45.000 0.50 0.00 0.00 2.78 R
7316 7960 0.971386 GTTGACCCCGACCTCTGTTA 59.029 55.000 0.00 0.00 0.00 2.41 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 4.467438 TGATGCCACTACTTCTGAAGATGA 59.533 41.667 23.36 7.65 0.00 2.92
93 94 6.205658 GCCACTACTTCTGAAGATGAACTTTT 59.794 38.462 23.36 0.85 39.13 2.27
149 150 4.500205 CCATTGCACCCACACATGATAATC 60.500 45.833 0.00 0.00 0.00 1.75
239 242 5.261209 TGATGGGTTGCATTTACTATTGC 57.739 39.130 0.00 0.00 39.33 3.56
240 243 4.708909 TGATGGGTTGCATTTACTATTGCA 59.291 37.500 0.00 0.00 46.51 4.08
248 251 6.696441 TGCATTTACTATTGCACATGATGA 57.304 33.333 0.00 0.00 43.54 2.92
249 252 7.279750 TGCATTTACTATTGCACATGATGAT 57.720 32.000 0.00 0.00 43.54 2.45
250 253 7.718525 TGCATTTACTATTGCACATGATGATT 58.281 30.769 0.00 0.00 43.54 2.57
251 254 8.198778 TGCATTTACTATTGCACATGATGATTT 58.801 29.630 0.00 0.00 43.54 2.17
252 255 9.037737 GCATTTACTATTGCACATGATGATTTT 57.962 29.630 0.00 0.00 38.72 1.82
294 297 4.730657 CTTGCTTCTCCTACTTGCAATTG 58.269 43.478 0.00 0.00 41.76 2.32
295 298 2.489329 TGCTTCTCCTACTTGCAATTGC 59.511 45.455 23.69 23.69 42.50 3.56
328 331 2.814336 GACAAGAACCACATCTTCACCC 59.186 50.000 0.00 0.00 37.56 4.61
415 420 1.450848 CATGACGGTGAGCCTGCAT 60.451 57.895 0.00 0.00 0.00 3.96
467 472 0.803117 CTACTTCCAGCGACGTCTCA 59.197 55.000 14.70 0.00 0.00 3.27
470 475 0.318699 CTTCCAGCGACGTCTCACAA 60.319 55.000 14.70 0.00 0.00 3.33
522 527 2.175184 CTTGCAGCACGGGAAACTCG 62.175 60.000 0.00 0.00 0.00 4.18
533 538 1.298859 GGAAACTCGCCAATCACGCT 61.299 55.000 0.00 0.00 0.00 5.07
549 554 2.249309 CTGCGTTGCAACACCGAG 59.751 61.111 28.01 13.09 38.41 4.63
551 556 4.683334 GCGTTGCAACACCGAGGC 62.683 66.667 28.01 18.07 0.00 4.70
552 557 4.368808 CGTTGCAACACCGAGGCG 62.369 66.667 28.01 8.82 0.00 5.52
567 574 2.746375 GGCGGGATGAGATGGTGGT 61.746 63.158 0.00 0.00 0.00 4.16
590 597 1.286880 GGACGCACATGCAGCTTTT 59.713 52.632 4.49 0.00 42.21 2.27
591 598 1.005294 GGACGCACATGCAGCTTTTG 61.005 55.000 4.49 0.00 42.21 2.44
609 616 4.908601 TTTGTGGAGGAGAAAGCTCATA 57.091 40.909 0.00 0.00 43.14 2.15
614 621 2.105477 GGAGGAGAAAGCTCATATGCCA 59.895 50.000 0.00 0.00 43.14 4.92
646 655 1.854280 AGAGAGGTAGGGGACGAAGAT 59.146 52.381 0.00 0.00 0.00 2.40
656 665 2.151202 GGGACGAAGATGTCAAAGCAA 58.849 47.619 0.00 0.00 40.72 3.91
660 669 1.135972 CGAAGATGTCAAAGCAACGGG 60.136 52.381 0.00 0.00 0.00 5.28
698 707 3.817084 CTGTGAAGTTGCATGGAGAGAAA 59.183 43.478 0.00 0.00 0.00 2.52
712 721 2.364002 GAGAGAAAGAGGATAAGCGGCT 59.636 50.000 0.00 0.00 0.00 5.52
726 735 4.115199 GGCTGGTGGGCCCTACAG 62.115 72.222 30.54 30.54 45.92 2.74
747 756 2.514013 CGTATGTTGCGCGAGGGAC 61.514 63.158 12.10 2.06 0.00 4.46
771 780 4.183865 CGGCTGATTTGTCTAGACATCAA 58.816 43.478 25.68 18.02 41.52 2.57
773 782 4.937620 GGCTGATTTGTCTAGACATCAACA 59.062 41.667 25.68 19.72 41.52 3.33
790 799 6.603997 ACATCAACAGGTTGGTTTAAACACTA 59.396 34.615 19.57 3.17 40.78 2.74
791 800 7.122948 ACATCAACAGGTTGGTTTAAACACTAA 59.877 33.333 19.57 8.84 40.78 2.24
792 801 7.648039 TCAACAGGTTGGTTTAAACACTAAT 57.352 32.000 19.57 0.21 40.78 1.73
793 802 8.068892 TCAACAGGTTGGTTTAAACACTAATT 57.931 30.769 19.57 7.30 40.78 1.40
794 803 8.532819 TCAACAGGTTGGTTTAAACACTAATTT 58.467 29.630 19.57 2.25 40.78 1.82
796 805 9.727859 AACAGGTTGGTTTAAACACTAATTTTT 57.272 25.926 19.57 1.66 0.00 1.94
827 842 4.150980 CGTAGCACGTTTCACTTTATGGAA 59.849 41.667 0.00 0.00 36.74 3.53
840 855 6.205853 TCACTTTATGGAATACACCACAACAC 59.794 38.462 0.00 0.00 43.03 3.32
841 856 6.016693 CACTTTATGGAATACACCACAACACA 60.017 38.462 0.00 0.00 43.03 3.72
842 857 6.719370 ACTTTATGGAATACACCACAACACAT 59.281 34.615 0.00 0.00 43.03 3.21
844 859 8.815565 TTTATGGAATACACCACAACACATAT 57.184 30.769 0.00 0.00 43.03 1.78
991 1020 4.430765 CAAGGGGACGGACGGACG 62.431 72.222 0.00 0.00 40.31 4.79
1228 1259 7.753309 TTTTGTCCCAAATCGAAATCTTCTA 57.247 32.000 0.00 0.00 0.00 2.10
1420 1451 0.754957 AGATGAGTCCGCCTCCTCAG 60.755 60.000 7.84 0.00 40.77 3.35
1445 1476 1.466856 TGATTTGCCAGATGCCACTC 58.533 50.000 0.00 0.00 40.16 3.51
1468 1499 2.362503 TCTGCGTCCGATCCCAGT 60.363 61.111 0.00 0.00 0.00 4.00
1482 1513 0.322008 CCCAGTCAGAAGCCTGGTTC 60.322 60.000 5.09 0.91 45.61 3.62
1487 1518 1.531578 GTCAGAAGCCTGGTTCGTTTC 59.468 52.381 3.66 0.00 40.76 2.78
1491 1522 2.002018 AAGCCTGGTTCGTTTCCCCA 62.002 55.000 0.00 0.00 0.00 4.96
1552 2023 2.723124 TTTCCTGATCTTTTTGCGCC 57.277 45.000 4.18 0.00 0.00 6.53
1808 2279 5.505181 AAGATCAGGTACATGTTCTTGGT 57.495 39.130 25.23 7.34 37.67 3.67
2118 2589 1.912043 CAGGGAGGGAGAATCACAAGT 59.088 52.381 0.00 0.00 45.06 3.16
2133 2604 9.288576 AGAATCACAAGTTTCATCTCAACAATA 57.711 29.630 0.00 0.00 0.00 1.90
2162 2633 2.346766 TGAGCTCCTTTCACTTGCAA 57.653 45.000 12.15 0.00 0.00 4.08
2505 2984 4.767255 GCTGCACGCTGCCCTAGT 62.767 66.667 9.51 0.00 44.23 2.57
2605 3084 3.486108 CGCGTATTGTCTTACAGATCACC 59.514 47.826 0.00 0.00 0.00 4.02
2861 3374 9.410556 ACTATTTGTTTATTCAAGTTGCATGAC 57.589 29.630 0.00 0.00 0.00 3.06
2864 3377 5.771469 TGTTTATTCAAGTTGCATGACAGG 58.229 37.500 0.00 0.00 0.00 4.00
2896 3409 4.405756 ACTCCCTCCGATCCATATTACT 57.594 45.455 0.00 0.00 0.00 2.24
3007 3572 5.416952 AGGCTTGAACTTTGGATAGTCATTG 59.583 40.000 0.00 0.00 0.00 2.82
3054 3619 2.439409 TGCAGCAATGCAGATTACACT 58.561 42.857 8.35 0.00 40.23 3.55
3086 3651 8.136800 GGTATTAGTGTTTAGGAGCTAGAACTC 58.863 40.741 0.00 0.00 35.86 3.01
3109 3674 7.071698 ACTCTGAGGCCTTTATAGATCAATTGA 59.928 37.037 6.77 11.26 0.00 2.57
3176 3741 7.581213 AATGTAAGACCATTTTTGACACTCA 57.419 32.000 0.00 0.00 31.01 3.41
3177 3742 7.765695 ATGTAAGACCATTTTTGACACTCAT 57.234 32.000 0.00 0.00 0.00 2.90
3178 3743 8.862325 ATGTAAGACCATTTTTGACACTCATA 57.138 30.769 0.00 0.00 0.00 2.15
3179 3744 8.094798 TGTAAGACCATTTTTGACACTCATAC 57.905 34.615 0.00 0.00 0.00 2.39
3180 3745 7.717436 TGTAAGACCATTTTTGACACTCATACA 59.283 33.333 0.00 0.00 0.00 2.29
3238 3803 9.950680 TTTTCTGTTCTGACTAATCAATCAAAC 57.049 29.630 0.00 0.00 33.30 2.93
3242 3807 8.853077 TGTTCTGACTAATCAATCAAACTGAT 57.147 30.769 0.00 0.00 39.09 2.90
3284 3849 1.562942 TCTCTTCCTCCTGCATTGCAT 59.437 47.619 12.53 0.00 38.13 3.96
3362 3927 4.667262 TGTATATTGACACGCAAAATGCC 58.333 39.130 0.00 0.00 41.12 4.40
3454 4019 8.986477 ATCCTGTGTTGTTTCTTTTATATTGC 57.014 30.769 0.00 0.00 0.00 3.56
3458 4023 9.409312 CTGTGTTGTTTCTTTTATATTGCATGA 57.591 29.630 0.00 0.00 0.00 3.07
3507 4072 4.640771 TTTATGCAGGTGGTCTCTTCTT 57.359 40.909 0.00 0.00 0.00 2.52
3765 4331 1.671261 CCAGTTCTCAGCAAGACTCCG 60.671 57.143 0.00 0.00 32.27 4.63
3834 4400 1.407575 GGTAGCAAAGGAGCCTCTTCC 60.408 57.143 0.00 0.00 37.52 3.46
3864 4430 3.561503 GTTTATGAAACGGGTTGCAGAC 58.438 45.455 0.00 0.00 30.39 3.51
3903 4469 4.727332 TCAGGAGTAATCAGAGGAGACCTA 59.273 45.833 0.00 0.00 31.76 3.08
3961 4527 5.163774 GCAGGTGATCACTTCTTTTCATCTC 60.164 44.000 24.50 3.98 27.14 2.75
4018 4584 6.762661 TCTTTGATCGTATGAAATCTGCATGA 59.237 34.615 0.00 0.00 0.00 3.07
4120 4686 3.332187 TGATGATTTGTGTTGTAGGGGGA 59.668 43.478 0.00 0.00 0.00 4.81
4276 4842 3.019564 GCTAGCTTCATCACCCAACAAT 58.980 45.455 7.70 0.00 0.00 2.71
4365 4931 7.800092 AGATTAAGTCATGCTAACTCCTGATT 58.200 34.615 0.00 0.00 0.00 2.57
4420 4986 7.778853 ACAAATCATATGAAAGAAGCAGATCCT 59.221 33.333 9.99 0.00 0.00 3.24
4547 5115 3.902261 TCACATGTTTAGCAACAGCTG 57.098 42.857 13.48 13.48 46.25 4.24
4560 5128 4.430137 CAACAGCTGCACTTGATACATT 57.570 40.909 15.27 0.00 0.00 2.71
4592 5160 7.210718 ACTGGTTATTTGGTTAACTGTTAGC 57.789 36.000 5.42 5.92 33.49 3.09
4593 5161 7.002276 ACTGGTTATTTGGTTAACTGTTAGCT 58.998 34.615 13.01 0.00 33.49 3.32
4594 5162 7.174426 ACTGGTTATTTGGTTAACTGTTAGCTC 59.826 37.037 13.01 5.49 33.49 4.09
4595 5163 6.148150 TGGTTATTTGGTTAACTGTTAGCTCG 59.852 38.462 13.01 0.00 33.49 5.03
4596 5164 6.369615 GGTTATTTGGTTAACTGTTAGCTCGA 59.630 38.462 13.01 2.68 33.49 4.04
4597 5165 7.095102 GGTTATTTGGTTAACTGTTAGCTCGAA 60.095 37.037 13.01 9.84 33.49 3.71
4598 5166 8.448615 GTTATTTGGTTAACTGTTAGCTCGAAT 58.551 33.333 13.01 14.54 0.00 3.34
4619 5187 3.791953 TCTTAGATCCCTCTAGTCGGG 57.208 52.381 12.08 12.08 43.38 5.14
4639 5207 9.618890 AGTCGGGAAAATATTCATGATATATGG 57.381 33.333 0.00 0.00 37.29 2.74
4684 5252 8.929827 TTTAGTAGTGCTATTTACGTTATGCA 57.070 30.769 0.00 0.00 0.00 3.96
4690 5258 5.783654 GTGCTATTTACGTTATGCATAAGCG 59.216 40.000 25.90 25.90 46.23 4.68
4809 5379 6.047511 AGCATGTTATGACATCCCTATCTC 57.952 41.667 0.00 0.00 44.55 2.75
5063 5634 6.521942 GCCCCTCTATTTTCCGATTAAGGTAT 60.522 42.308 0.00 0.00 0.00 2.73
5078 5649 4.634012 AAGGTATGGTGTTTCTGTGCTA 57.366 40.909 0.00 0.00 0.00 3.49
5085 5656 9.284968 GGTATGGTGTTTCTGTGCTATATAAAT 57.715 33.333 0.00 0.00 0.00 1.40
5136 5708 4.556104 GCCATATGATTGCTAACTGCTGTG 60.556 45.833 3.65 0.00 43.37 3.66
5346 5918 7.757097 TCTAATAACTCAAAAGATCAGTCGC 57.243 36.000 0.00 0.00 0.00 5.19
5375 5947 3.129813 TGCTTGGTACACCATCTAGTACG 59.870 47.826 1.05 0.00 46.97 3.67
5460 6032 3.761218 TCAAGAACAAGTTCCTGCAAACA 59.239 39.130 9.20 0.00 40.33 2.83
5693 6266 2.027192 TGTGAAGTGACCTCTATTGCCC 60.027 50.000 0.00 0.00 0.00 5.36
5801 6374 0.179037 GCAGCCAGCTCATACATCCA 60.179 55.000 0.00 0.00 41.15 3.41
6082 6655 4.036027 GGTAATCCTTGTGCTGATGATGTG 59.964 45.833 0.00 0.00 0.00 3.21
6165 6738 3.222173 AGATCAGCCTCTAGATGACGT 57.778 47.619 0.00 0.00 0.00 4.34
6259 6832 7.526608 TGCCGAGACTTACATTTTTATCTTTG 58.473 34.615 0.00 0.00 0.00 2.77
6736 7311 2.622942 TGTGAAATGAGCTTGGGTCAAC 59.377 45.455 3.59 0.00 43.29 3.18
6878 7453 8.819974 CATAAATCAATGTGTTTATTTGAGGGC 58.180 33.333 4.54 0.00 30.32 5.19
6940 7515 4.202151 GGGTCAATGTTTTAGATGGATGGC 60.202 45.833 0.00 0.00 0.00 4.40
6981 7556 2.285083 CCATCGAATCAAAGCCGGTTA 58.715 47.619 1.90 0.00 0.00 2.85
7061 7636 8.608598 AGCTAAAAGGTAGGTTTTTATAGGACA 58.391 33.333 0.00 0.00 31.66 4.02
7170 7791 5.474532 CCACAAAAGAAAGGATCAGACATGA 59.525 40.000 0.00 0.00 40.50 3.07
7216 7837 6.775629 AGTTGAGGTAGCACCAATTTAAAGAA 59.224 34.615 7.86 0.00 41.95 2.52
7259 7903 4.022416 TGAGTTGGTTTGGACATATGCAAC 60.022 41.667 1.58 7.25 35.65 4.17
7273 7917 3.855689 ATGCAACACAAGCCTTCATAC 57.144 42.857 0.00 0.00 0.00 2.39
7305 7949 0.168128 AGCGAATGGTTAAAGCGTGC 59.832 50.000 0.00 0.00 0.00 5.34
7315 7959 4.457603 TGGTTAAAGCGTGCTGATAATGTT 59.542 37.500 0.00 0.00 0.00 2.71
7316 7960 5.048364 TGGTTAAAGCGTGCTGATAATGTTT 60.048 36.000 0.00 0.00 0.00 2.83
7338 7982 1.273098 ACAGAGGTCGGGGTCAACTAT 60.273 52.381 0.00 0.00 0.00 2.12
7379 8023 3.454812 GGCCCCTTCTAGATAGTTTGTGA 59.545 47.826 0.00 0.00 0.00 3.58
7455 8101 0.935942 TTGGCATCAATCCATCCCCT 59.064 50.000 0.00 0.00 32.92 4.79
7583 8235 9.950680 ATTAATTGAGTAAACTTTGACACACAG 57.049 29.630 0.00 0.00 0.00 3.66
7735 8418 7.602644 TCTGTTGAAATATTCGCTTCTACAGTT 59.397 33.333 19.64 0.00 46.42 3.16
7736 8419 7.739295 TGTTGAAATATTCGCTTCTACAGTTC 58.261 34.615 0.00 0.00 34.06 3.01
7737 8420 7.386573 TGTTGAAATATTCGCTTCTACAGTTCA 59.613 33.333 0.00 0.00 34.06 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.327104 TGGATATTTCAAATGAATCCAAGGGG 59.673 38.462 10.97 0.00 37.62 4.79
23 24 6.619874 GCAAGCATCAAGTTCATCAAAAATGG 60.620 38.462 0.00 0.00 0.00 3.16
126 127 1.187974 ATCATGTGTGGGTGCAATGG 58.812 50.000 0.00 0.00 0.00 3.16
226 229 8.583810 AAATCATCATGTGCAATAGTAAATGC 57.416 30.769 0.00 4.74 42.86 3.56
233 236 9.923143 ATCCATTAAAATCATCATGTGCAATAG 57.077 29.630 0.00 0.00 0.00 1.73
246 249 9.642327 GCACATGCATAATATCCATTAAAATCA 57.358 29.630 0.00 0.00 41.59 2.57
247 250 9.865321 AGCACATGCATAATATCCATTAAAATC 57.135 29.630 6.64 0.00 45.16 2.17
249 252 9.478768 CAAGCACATGCATAATATCCATTAAAA 57.521 29.630 6.64 0.00 45.16 1.52
250 253 7.599621 GCAAGCACATGCATAATATCCATTAAA 59.400 33.333 6.64 0.00 45.70 1.52
251 254 7.092079 GCAAGCACATGCATAATATCCATTAA 58.908 34.615 6.64 0.00 45.70 1.40
252 255 6.623486 GCAAGCACATGCATAATATCCATTA 58.377 36.000 6.64 0.00 45.70 1.90
253 256 5.475719 GCAAGCACATGCATAATATCCATT 58.524 37.500 6.64 0.00 45.70 3.16
254 257 5.068234 GCAAGCACATGCATAATATCCAT 57.932 39.130 6.64 0.00 45.70 3.41
255 258 4.508461 GCAAGCACATGCATAATATCCA 57.492 40.909 6.64 0.00 45.70 3.41
294 297 6.128391 TGTGGTTCTTGTCTCGTAATAATTGC 60.128 38.462 0.00 0.00 0.00 3.56
295 298 7.359262 TGTGGTTCTTGTCTCGTAATAATTG 57.641 36.000 0.00 0.00 0.00 2.32
296 299 8.041323 AGATGTGGTTCTTGTCTCGTAATAATT 58.959 33.333 0.00 0.00 0.00 1.40
297 300 7.556844 AGATGTGGTTCTTGTCTCGTAATAAT 58.443 34.615 0.00 0.00 0.00 1.28
299 302 6.525578 AGATGTGGTTCTTGTCTCGTAATA 57.474 37.500 0.00 0.00 0.00 0.98
300 303 5.407407 AGATGTGGTTCTTGTCTCGTAAT 57.593 39.130 0.00 0.00 0.00 1.89
301 304 4.866508 AGATGTGGTTCTTGTCTCGTAA 57.133 40.909 0.00 0.00 0.00 3.18
302 305 4.279922 TGAAGATGTGGTTCTTGTCTCGTA 59.720 41.667 0.00 0.00 36.10 3.43
303 306 3.069586 TGAAGATGTGGTTCTTGTCTCGT 59.930 43.478 0.00 0.00 36.10 4.18
304 307 3.430218 GTGAAGATGTGGTTCTTGTCTCG 59.570 47.826 0.00 0.00 36.10 4.04
311 314 1.630878 GAGGGGTGAAGATGTGGTTCT 59.369 52.381 0.00 0.00 0.00 3.01
415 420 0.541392 ATGCTACAATGTCCGCCTGA 59.459 50.000 0.00 0.00 0.00 3.86
425 430 1.666209 GGCGTTGCCCATGCTACAAT 61.666 55.000 0.00 0.00 44.06 2.71
463 468 1.300931 GCTCGCCAGTGTTGTGAGA 60.301 57.895 12.48 0.00 30.53 3.27
467 472 3.537206 GAGGGCTCGCCAGTGTTGT 62.537 63.158 10.51 0.00 37.98 3.32
470 475 4.008933 GTGAGGGCTCGCCAGTGT 62.009 66.667 10.51 0.00 37.98 3.55
522 527 2.502510 CAACGCAGCGTGATTGGC 60.503 61.111 23.78 0.00 39.99 4.52
533 538 3.276091 CCTCGGTGTTGCAACGCA 61.276 61.111 36.23 20.88 44.89 5.24
549 554 2.111878 CCACCATCTCATCCCGCC 59.888 66.667 0.00 0.00 0.00 6.13
551 556 0.462581 CACACCACCATCTCATCCCG 60.463 60.000 0.00 0.00 0.00 5.14
552 557 0.107017 CCACACCACCATCTCATCCC 60.107 60.000 0.00 0.00 0.00 3.85
555 560 0.549902 TCCCCACACCACCATCTCAT 60.550 55.000 0.00 0.00 0.00 2.90
590 597 3.432749 GCATATGAGCTTTCTCCTCCACA 60.433 47.826 6.97 0.00 38.58 4.17
591 598 3.137533 GCATATGAGCTTTCTCCTCCAC 58.862 50.000 6.97 0.00 38.58 4.02
609 616 4.286549 CCTCTCTCTAATGGATCTTGGCAT 59.713 45.833 0.00 0.00 0.00 4.40
614 621 5.460423 CCCCTACCTCTCTCTAATGGATCTT 60.460 48.000 0.00 0.00 0.00 2.40
646 655 1.228124 CCTCCCCGTTGCTTTGACA 60.228 57.895 0.00 0.00 0.00 3.58
656 665 1.409661 GCCACATATTTTCCTCCCCGT 60.410 52.381 0.00 0.00 0.00 5.28
660 669 3.620488 TCACAGCCACATATTTTCCTCC 58.380 45.455 0.00 0.00 0.00 4.30
698 707 1.690219 CCACCAGCCGCTTATCCTCT 61.690 60.000 0.00 0.00 0.00 3.69
712 721 2.609610 GTCCTGTAGGGCCCACCA 60.610 66.667 27.56 18.90 43.89 4.17
726 735 2.514013 CCTCGCGCAACATACGTCC 61.514 63.158 8.75 0.00 0.00 4.79
747 756 0.924090 GTCTAGACAAATCAGCCGCG 59.076 55.000 18.20 0.00 0.00 6.46
790 799 5.739237 CGTGCTACGCAACAATAAAAATT 57.261 34.783 0.00 0.00 41.47 1.82
817 832 6.065374 TGTGTTGTGGTGTATTCCATAAAGT 58.935 36.000 0.00 0.00 39.54 2.66
821 836 9.500785 CATATATGTGTTGTGGTGTATTCCATA 57.499 33.333 4.43 0.00 39.81 2.74
827 842 6.828273 AGTTGCATATATGTGTTGTGGTGTAT 59.172 34.615 14.14 0.00 0.00 2.29
997 1026 3.988050 TATTGGACCCTCGGCCGGT 62.988 63.158 27.83 16.15 35.88 5.28
1000 1029 2.509422 GGTATTGGACCCTCGGCC 59.491 66.667 0.00 0.00 43.25 6.13
1420 1451 1.738030 GCATCTGGCAAATCAACAGGC 60.738 52.381 0.00 0.00 43.97 4.85
1468 1499 1.542547 GGAAACGAACCAGGCTTCTGA 60.543 52.381 0.00 0.00 40.86 3.27
1482 1513 0.955905 AACGAAATGGTGGGGAAACG 59.044 50.000 0.00 0.00 0.00 3.60
1487 1518 1.680989 GGGGAACGAAATGGTGGGG 60.681 63.158 0.00 0.00 0.00 4.96
1491 1522 1.905637 GTTCAGGGGAACGAAATGGT 58.094 50.000 0.00 0.00 43.54 3.55
1552 2023 6.690098 CCTTTTTCGCTATCAAGATGAACATG 59.310 38.462 0.00 0.00 0.00 3.21
2015 2486 3.630625 AGGGGATAGTGGTGCTATGTA 57.369 47.619 0.00 0.00 40.30 2.29
2133 2604 4.639310 GTGAAAGGAGCTCATCATCATTGT 59.361 41.667 17.19 0.00 0.00 2.71
2162 2633 0.042131 TGTAAGGAGGGGACATCGGT 59.958 55.000 0.00 0.00 0.00 4.69
2505 2984 2.573369 TGGCCAGTTTAACACGCTTTA 58.427 42.857 0.00 0.00 0.00 1.85
2896 3409 5.079689 TCCATATTACTTGTCGCTCACAA 57.920 39.130 0.00 0.00 43.12 3.33
3007 3572 7.900782 ATATACCGCATGATTTGTAGGTTAC 57.099 36.000 0.00 0.00 38.68 2.50
3054 3619 5.104652 GCTCCTAAACACTAATACCCCAGAA 60.105 44.000 0.00 0.00 0.00 3.02
3086 3651 7.222872 ACTCAATTGATCTATAAAGGCCTCAG 58.777 38.462 5.23 0.97 0.00 3.35
3175 3740 4.202441 CTCCCTCTGTCCCAAAATGTATG 58.798 47.826 0.00 0.00 0.00 2.39
3176 3741 3.852578 ACTCCCTCTGTCCCAAAATGTAT 59.147 43.478 0.00 0.00 0.00 2.29
3177 3742 3.256704 ACTCCCTCTGTCCCAAAATGTA 58.743 45.455 0.00 0.00 0.00 2.29
3178 3743 2.065799 ACTCCCTCTGTCCCAAAATGT 58.934 47.619 0.00 0.00 0.00 2.71
3179 3744 2.887151 ACTCCCTCTGTCCCAAAATG 57.113 50.000 0.00 0.00 0.00 2.32
3180 3745 5.491078 TGTAATACTCCCTCTGTCCCAAAAT 59.509 40.000 0.00 0.00 0.00 1.82
3284 3849 9.976776 TCCACACCCAGTTATTGTTATTAATTA 57.023 29.630 0.00 0.00 0.00 1.40
3469 4034 8.491152 CCTGCATAAAACTCAGTTATTATCTCG 58.509 37.037 0.00 0.00 0.00 4.04
3476 4041 5.570320 ACCACCTGCATAAAACTCAGTTAT 58.430 37.500 0.00 0.00 0.00 1.89
3507 4072 3.415212 AGCACTGCAGCTAAATTTCTCA 58.585 40.909 15.27 0.00 44.50 3.27
3684 4250 5.986004 TTCTTCTCGTTCTTTTTCTGTCC 57.014 39.130 0.00 0.00 0.00 4.02
3765 4331 4.035675 CCTACTGCGAAAGATTGATTTCCC 59.964 45.833 0.00 0.00 36.08 3.97
3813 4379 1.279271 GAAGAGGCTCCTTTGCTACCA 59.721 52.381 11.71 0.00 0.00 3.25
3864 4430 6.301169 ACTCCTGACTTGTTAGAATTAGGG 57.699 41.667 0.00 0.00 0.00 3.53
3961 4527 9.160496 GAGGCTAAGGATACATCATATCAAAAG 57.840 37.037 0.00 0.00 41.41 2.27
4073 4639 7.227314 CAGCTATCAACACTAATGCAAGGAATA 59.773 37.037 0.00 0.00 0.00 1.75
4276 4842 9.378551 GAAACAATACCATCAACAGTAGATACA 57.621 33.333 0.00 0.00 0.00 2.29
4388 4954 7.560991 TGCTTCTTTCATATGATTTGTACCCAT 59.439 33.333 6.17 0.00 0.00 4.00
4393 4959 9.060347 GGATCTGCTTCTTTCATATGATTTGTA 57.940 33.333 6.17 0.00 0.00 2.41
4517 5083 7.010923 TGTTGCTAAACATGTGATTGGTTTTTC 59.989 33.333 0.00 0.00 41.41 2.29
4547 5115 9.326413 ACCAGTAATAACTAATGTATCAAGTGC 57.674 33.333 0.00 0.00 33.48 4.40
4592 5160 6.128391 CGACTAGAGGGATCTAAGAATTCGAG 60.128 46.154 0.00 2.01 0.00 4.04
4593 5161 5.701750 CGACTAGAGGGATCTAAGAATTCGA 59.298 44.000 0.00 0.00 0.00 3.71
4594 5162 5.106475 CCGACTAGAGGGATCTAAGAATTCG 60.106 48.000 0.00 0.00 0.00 3.34
4595 5163 6.262193 CCGACTAGAGGGATCTAAGAATTC 57.738 45.833 0.00 0.00 0.00 2.17
4677 5245 4.856487 TGCAGAAAAACGCTTATGCATAAC 59.144 37.500 15.21 11.06 45.79 1.89
4680 5248 3.574284 TGCAGAAAAACGCTTATGCAT 57.426 38.095 3.79 3.79 45.79 3.96
4684 5252 2.228822 CCCACTGCAGAAAAACGCTTAT 59.771 45.455 23.35 0.00 0.00 1.73
4809 5379 8.985922 TGGATTATGATCATCCTGTTATAGAGG 58.014 37.037 12.53 0.00 40.99 3.69
5003 5574 0.399454 AGACATCAGCCACTGCAACT 59.601 50.000 0.00 0.00 41.13 3.16
5085 5656 7.723324 GCCACTAATGGTCTAGAACATTACTA 58.277 38.462 30.81 18.29 46.06 1.82
5086 5657 6.583562 GCCACTAATGGTCTAGAACATTACT 58.416 40.000 30.81 22.06 46.06 2.24
5087 5658 6.846325 GCCACTAATGGTCTAGAACATTAC 57.154 41.667 30.81 20.64 46.06 1.89
5136 5708 6.921307 CCATACCTTACCAACAAAAAGTTCAC 59.079 38.462 0.00 0.00 38.74 3.18
5460 6032 5.478332 CAGGAATAAGGACCTCAAAAGCTTT 59.522 40.000 5.69 5.69 33.91 3.51
5693 6266 7.192232 GGATTCTCATCGAAAAGAGGATTTTG 58.808 38.462 11.45 0.00 39.12 2.44
6082 6655 4.301628 CACAAAGTTCTTCCATTGCCTTC 58.698 43.478 0.00 0.00 0.00 3.46
6165 6738 5.279809 GGGCATTCGTCTAATACCCAGAATA 60.280 44.000 1.23 0.00 46.94 1.75
6259 6832 2.217429 TTCGGGCTGCAAAAAGAAAC 57.783 45.000 0.50 0.00 0.00 2.78
6308 6881 5.158141 TCATCAGCTAGGGATCTTATTGGT 58.842 41.667 0.00 0.00 0.00 3.67
6593 7166 0.518636 CAACAACATGCGTCCCTCTG 59.481 55.000 0.00 0.00 0.00 3.35
6940 7515 6.908870 TGGTTCTTATCTTCATCAACATCG 57.091 37.500 0.00 0.00 0.00 3.84
6981 7556 2.770164 AACTTAGCGCCACTTCATCT 57.230 45.000 2.29 0.00 0.00 2.90
7053 7628 3.250280 GTGAGTCGAATCGCTGTCCTATA 59.750 47.826 18.42 0.00 0.00 1.31
7061 7636 2.370281 ACATTGTGAGTCGAATCGCT 57.630 45.000 24.71 5.23 0.00 4.93
7117 7738 1.133598 CCATCGCAACATGCACATCTT 59.866 47.619 2.99 0.00 45.36 2.40
7170 7791 7.549134 TCAACTCTCTTGCGTATATCAACATTT 59.451 33.333 0.00 0.00 0.00 2.32
7186 7807 2.609747 TGGTGCTACCTCAACTCTCTT 58.390 47.619 6.83 0.00 39.58 2.85
7216 7837 8.517878 CAACTCAGATGATGTTGGATAAACTTT 58.482 33.333 13.08 0.00 39.70 2.66
7233 7854 4.641989 GCATATGTCCAAACCAACTCAGAT 59.358 41.667 4.29 0.00 0.00 2.90
7292 7936 4.006989 ACATTATCAGCACGCTTTAACCA 58.993 39.130 0.00 0.00 0.00 3.67
7305 7949 5.523916 CCCGACCTCTGTTAAACATTATCAG 59.476 44.000 0.00 3.03 0.00 2.90
7315 7959 1.345415 GTTGACCCCGACCTCTGTTAA 59.655 52.381 0.00 0.00 0.00 2.01
7316 7960 0.971386 GTTGACCCCGACCTCTGTTA 59.029 55.000 0.00 0.00 0.00 2.41
7338 7982 2.163412 GCCTTGGTTACGATGCATTTCA 59.837 45.455 0.00 0.00 0.00 2.69
7395 8039 1.852633 AAAACAGCTTATGGCCTCCC 58.147 50.000 3.32 0.00 43.05 4.30
7583 8235 2.719426 AGTACCTCGTGTTAGTGTGC 57.281 50.000 0.00 0.00 0.00 4.57
7735 8418 5.073428 ACTCTATATCGGTGCTCTCAATGA 58.927 41.667 0.00 0.00 0.00 2.57
7736 8419 5.384063 ACTCTATATCGGTGCTCTCAATG 57.616 43.478 0.00 0.00 0.00 2.82
7737 8420 4.461081 GGACTCTATATCGGTGCTCTCAAT 59.539 45.833 0.00 0.00 0.00 2.57



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.